haplo.stats v1.7.9

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Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous

Routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main functions are: haplo.em(), haplo.glm(), haplo.score(), and haplo.power(); all of which have detailed examples in the vignette.

Functions in haplo.stats

Name Description
geno.count.pairs Counts of Total Haplotype Pairs Produced by Genotypes
get.hapPair Get a list of objects for haplotype pairs
hapPower.demo Set of haplotypes and frequencies for power and sample size calculations
haplo.hash Integer Rank Codes for Haplotypes
haplo.scan Search for a trait-locus by sliding a fixed-width window over each marker locus and scanning all possible haplotype lengths within the window
haplo.em.fitter Compute engine for haplotype EM algorithm
summary.haplo.glm Print and summary of a haplo.glm object
anova.haplo.glm Analysis of variance for haplo.glm model fit
Ginv Compute Generalized Inverse of Input Matrix
haplo.glm GLM Regression of Trait on Ambiguous Haplotypes
haplo.model.frame Sets up a model frame for haplo.glm
haplo.score.merge Merge haplo.score And haplo.group Objects
haplo.score Score Statistics for Association of Traits with Haplotypes
haplo.score.slide Score Statistics for Association of Traits with Haplotypes
print.haplo.em Print contents of a haplo.em object
find.haplo.beta.qt Find beta coefficients for risk haplotypes, for specified r2
print.haplo.scan Print a haplo.scan object
print.haplo.group Print a haplo.group object
fitted.haplo.glm Fitted values from haplo.glm fit
chisq.power Power and sample size for the chi-square distribution
printBanner Print a nice banner
haplo.design Build a design matrix for haplotypes
haplo.cc Haplotype Association Analysis in a Case-Control design
f.power Power and sample size for the F distribution
haplo.group Frequencies for Haplotypes by Grouping Variable
haplo.glm.control Create list of control parameters for haplo.glm
print.haplo.score Print a haplo.score object
residuals.haplo.glm Accessing residuals for haplo.glm fit
dglm.fit Internal functions for the HaploStats package. See the help file for the main functions (haplo.em, haplo.score, haplo.glm) for details on some of these functions.
hla.demo HLA Loci and Serologic Response to Measles Vaccination
locator.haplo Find Location from Mouse Clicks and Print Haplotypes on Plot
setupGeno Create a group of locus objects from a genotype matrix, assign to 'model.matrix' class.
locus Creates an object of class "locus"
plot.haplo.score Plot Haplotype Frequencies versus Haplotype Score Statistics
seqhap.dat Simulated data for seqhap examples
louis.info Louis Information for haplo.glm
plot.haplo.score.slide Plot a haplo.score.slide Object
score.sim.control Create the list of control parameters for simulations in haplo.score
x.sexcheck consistency checks for x.linked locus
na.geno.keep Remove rows with NA in covariates, but keep genotypes with NAs
seqhap Sequential Haplotype Scan Association Analysis for Case-Control Data
print.haplo.score.merge Print a haplo.score.merge object
print.haplo.score.slide Print the contents of a haplo.score.slide object
summaryGeno Summarize Full Haplotype Enumeration on Genotype Matrix
vcov.haplo.glm variance-covariance matrix of a fitted haplo.glm object
plot.seqhap Plot a seqhap object
print.haplo.cc Print a haplo.cc object
summary.haplo.em Summarize contents of a haplo.em object
geno1to2 convert genotype matrix from 1-column 2-column
haplo.em EM Computation of Haplotype Probabilities, with Progressive Insertion of Loci
haplo.em.control Create the Control Parameters for the EM Computation of Haplotype Probabilities, with Progressive Insertion of Loci
haplo.power.qt Compute either power or sample size for haplotype associations with a quantitative trait.
haplo.power.cc Compute either power or sample size for haplotype associations in a case-control study.
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Vignettes of haplo.stats

Name
manualHaploStats.pdf.asis
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Details

Date 2018-04-10
License GPL (>= 2)
VignetteBuilder R.rsp
URL http://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software
NeedsCompilation yes
Packaged 2018-04-11 13:18:13 UTC; sinnwell
Repository CRAN
Date/Publication 2018-04-11 14:13:58 UTC

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